org.string-db/string-mcp (MCP Server)

This Model Context Protocol (MCP) server exposes STRING database functionality as an MCP service. It enables MCP-compatible clients to query STRING interactions, enrichment, annotations, homology, and PPI networks via a structured, self-describing interface, built on the STRING API.

🛠️ Key Features

Access STRING interactions, enrichment, annotations, homology, and PPI networks
Exposes STRING database functionality through an MCP server interface
Built on top of the STRING API, adapted for model-based use
Controls response data amount/type for conciseness and context efficiency
Adds metadata and adapts response structure to support model use

🚀 Use Cases

Query STRING interactions
Retrieve enrichment and annotations from STRING
Perform homology lookups using STRING data
Explore PPI networks

⚡ Developer Benefits

Structured MCP access to STRING database capabilities
Self-describing interface for MCP-compatible clients
Response structure and metadata intended to support context for large language models

⚠️ Limitations

Implementation emphasizes conciseness and context efficiency, controlling response size to fit reasoning limits of large language models.

STRING MCP Server

Exposes STRING database functionality as a Model Context Protocol (MCP) server.

This implementation allows AI agents and other MCP-compatible clients to access STRING data through a structured and self-describing interface.

It is built on top of the STRING API but adapted specifically for model-based use, with emphasis on conciseness and context efficiency. The server controls the amount and type of data so that responses stay within the reasoning limits of large language models. It also adapts the structure and adds metadata to support more consistent parsing and interpretation by agentic systems.

The server is also available as a hosted remote MCP endpoint at https://mcp.string-db.org.

For a live demonstration of MCP capabilities, see STRING Chat.

For reproducible workflows and large-scale integration, use the STRING API.

For agentic workflows, use the optional agent skill at skills/string-database/SKILL.md.

Features

Resolve protein identifiers to STRING metadata
Retrieve interaction networks
Cluster and visualize interaction networks
Perform homology lookups across species
Access evidence links for protein–protein interactions
Run functional enrichment analysis (including enrichment plots)
Get curated functional annotations for proteins
Query proteins by function or disease (GO, KEGG, Reactome, DISEASES etc.)

Requirements

Python ≥ 3.10
Dependencies (see requirements.txt):
- fastmcp==2.10.6
- httpx==0.28.1
- pydantic==2.11.7

Note: If the server crashes on startup, it is very likely due to an incompatible FastMCP version.

Configuration

The server reads settings from config/server.config (JSON). Example:

json

{
  "base_url": "https://string-db.org",
  "server_port": 57416,
  "verbosity": "low"
}

Installation

bash

git clone https://github.com/meringlab/string-mcp.git
cd string-mcp
pip install -r requirements.txt

Running

code

python server.py

Testing

bash

curl -v -H "Accept: text/event-stream" http://localhost:[port]/mcp

You should see a 200 OK response with content-type: text/event-stream.

Note: HTTP requests sent with default headers will trigger anyio.ClosedResourceError and 406 Not Acceptable. This is expected behavior for the MCP streaming protocol and does not indicate a problem.

Docker

Ensure you have a config/server.config file (copy from config/server.config.example if needed):
bash
```
cp config/server.config.example config/server.config
```
Build the image:
bash
```
docker build -t string-mcp .
```

Run the container:

Linux/macOS:

bash

docker run -p 57416:57416 -v $(pwd)/config:/app/config:ro string-mcp

Windows PowerShell:

powershell

docker run -p 57416:57416 -v ${PWD}/config:/app/config:ro string-mcp

Windows Command Prompt:

cmd

docker run -p 57416:57416 -v %cd%/config:/app/config:ro string-mcp

To run in detached mode:

bash

# Linux/macOS
docker run -d -p 57416:57416 -v $(pwd)/config:/app/config:ro --name string-mcp-server string-mcp

# Windows PowerShell
docker run -d -p 57416:57416 -v ${PWD}/config:/app/config:ro --name string-mcp-server string-mcp

The -v flag mounts your local config directory so you can customize settings without rebuilding the image.

Note: If you don't need to modify the config, you can omit the volume mount and the container will use the default config from the image.

Stop the container (if running in detached mode):

bash

docker stop string-mcp-server
docker rm string-mcp-server

Note: The Docker container will use the configuration from config/server.config. If this file doesn't exist, the container will copy from server.config.example on first run.

STRING v12.0 is the frozen network release, available under the /v12.0/ path.

License / Citation

The STRING MCP server source code is released under the MIT License.
Associated data and outputs are released under the CC BY 4.0 License.
You are free to use, share, and modify the code with proper attribution.

If you use this code or data in your work, please also cite the latest STRING manuscript.

identifier_a	string	required	Required. Protein A identifier.
identifiers_b	string	required	Required. One or more protein B identifiers, separated by %0d.
species	any	optional

filename	string	required	Required. Suggested output filename with a safe extension such as .tsv, .csv, .json, .md, or .txt. Match content to the extension; prefer .tsv for reusable tabular STRING data. Use a concise name that reflects the STRING analysis result, for example string-enrichment.tsv.
content	string	required	Required STRING-derived file content. For .tsv/.csv: one rectangular table, one header row, matching delimiter, no Markdown/prose/repeated headers/multiple tables. Use one row per entity, edge, cluster member, annotation, or enrichment term. Use bare numeric scores/FDR/p-values; put interpretation and caveats in chat or .md/.txt.

STRING Database MCP Server

org.string-db/string-mcp (MCP Server)

🛠️ Key Features

🚀 Use Cases

⚡ Developer Benefits

⚠️ Limitations

string_resolve_proteins

string_interactions_query_set

string_all_interaction_partners

string_visual_network

string_network_clustering

string_network_link

string_homology

string_interaction_evidence

string_enrichment

string_functional_annotation

string_enrichment_image_url

string_ppi_enrichment

string_proteins_for_term

string_sequence_search

string_query_species

string_create_file

string_help

STRING MCP Server

Features

Requirements

Configuration

Installation

Running

Testing

Docker

License / Citation

Install

Remote endpoint

Related servers

proteins	string	required	Required. One or more input protein identifiers (gene symbols, UniProt IDs, etc.), separated by carriage return (%0d). Example: TP53%0dSMO
species	any	optional
show_sequence	any	optional

identifiers	string	required	Required. One or more protein identifiers, separated by carriage return (%0d). Example: TP53%0dSMO
species	any	optional
required_score	any	optional
network_type	any	optional

term_text	string	required	Required. Functional term identifier (GO, KEGG, Reactome, etc.) or descriptive free text (e.g. 'hsa05218', 'Melanoma', 'GO:0008543', 'Fibroblast growth factor').
species	string	optional	NCBI/STRING taxonomy ID. This tool only supports one species per call. It cannot return results across multiple species or identify the species with the most/fewest proteins. For such questions, run this tool separately for each species and then compare the results. Default is 9606 (human). Examples: 10090 for mouse, or STRG0AXXXXX for uploaded genomes.
detail_for_term	any	optional

sequences	string	required	One or more protein sequences in plain or FASTA format.For multiple sequences, use standard FASTA headers (lines beginning with '>'). Only amino acid sequences are supported — nucleotide sequences are not accepted.
species	string	optional	Required. NCBI or STRING taxonomy ID. You can query with a clade or species. eg.g 2 for bacteria, 7742 for vertebrates, 511145 for E. coli